GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Klebsiella michiganensis M5al

Align D-xylose transporter; D-xylose-proton symporter (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter

Query= SwissProt::O52733
         (457 letters)



>FitnessBrowser__Koxy:BWI76_RS03110
          Length = 499

 Score =  307 bits (787), Expect = 4e-88
 Identities = 180/449 (40%), Positives = 276/449 (61%), Gaps = 13/449 (2%)

Query: 9   VYFFGALGGLLFGYDTGVISGAILFIQKQMNLGSWQQGWVVSAVLLGAILGAAIIGPSSD 68
           V     LGGLLFGYDTGVISGA+LF+  +++L  +  G V S++L GA  GA + G  ++
Sbjct: 28  VALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVTSSLLFGAAFGALLSGNLAN 87

Query: 69  RFGRRKLLLLSAIIFFVGALGSAFSPEFWTLIISRIILGMAVGAASALIPTYLAELAPSD 128
             GR+K++L  A++F +GA+G++ +P+   +I  R+ILG+AVG A+A +P Y+AE+AP++
Sbjct: 88  AAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAVGGAAATVPVYIAEIAPAN 147

Query: 129 KRGTVSSLFQLMVMTGILLAYITNYSFSGFYTG---WRWMLGFAAIPAALLFLGGLILPE 185
           KRG + +L +LM+++G LLAYI+N +F   + G   WRWML  A +PA LL+ G + +P+
Sbjct: 148 KRGQLVTLQELMIVSGQLLAYISNATFHEVWGGESTWRWMLAVATLPAVLLWFGMMFMPD 207

Query: 186 SPRFLVKSGHLDEARHVLD-TMNKHDQVAVNKEIND-IQESAKIVSGGWSELFGKMVRPS 243
           SPR+    G L EAR VL+ T +K D      EI + + E   +    +SE+    +   
Sbjct: 208 SPRWYAMKGRLAEARRVLERTRHKDDVEWELLEITETLDEQRNLGKPRFSEIMTPWLFKL 267

Query: 244 LIIGIGLAIFQQVMGCNTVLYYAPTIFTDVGFGVSAALLAHIGIGIFNVIVTAIAVAIMD 303
            +IGIG+A+ QQ+ G NT++YYAPT+ T VG   +AAL A I  G+ +V++T + + ++ 
Sbjct: 268 FMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMTDNAALFATIANGVVSVLMTFVGIWMLG 327

Query: 304 KIDRKKIVNIGAVGMGISL-FVMSIGM---KFSGGSQTA--AIISVIALTVYIAFFSATW 357
           KI R+ +  IG  G    L F+ ++     +   G   A  A + +  + ++++F     
Sbjct: 328 KIGRRPMTMIGQFGCTACLVFIGAVSYLLPETVNGQPDALRAYMVLAGMLLFLSFQQGAL 387

Query: 358 GPVMWVMIGEVFPLNIRGLGNSFASVINWTANMIVSLTFPSLLDFFG-TGSLFIGYGILC 416
            PV W+++ E+FP  +RG+    A    W AN ++SL FP LL + G +G+ FI  GI  
Sbjct: 388 SPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANFLISLFFPILLAWLGLSGTFFIFAGIGV 447

Query: 417 FASIWFVQKKVFETRNRSLEDIEATLRAK 445
           F +I FV K V ETR+RSLE IE  LR K
Sbjct: 448 FGAI-FVIKCVPETRHRSLEQIEHYLRDK 475


Lambda     K      H
   0.327    0.141    0.424 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 622
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 457
Length of database: 499
Length adjustment: 34
Effective length of query: 423
Effective length of database: 465
Effective search space:   196695
Effective search space used:   196695
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory